Contacts of the helix formed by residues 52 - 61 (chain A) in PDB entry 1COZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.4 34.5 - - + -
36A SER 3.6 17.3 - - - -
37A THR* 3.7 10.8 - - + -
38A ASP* 3.1 27.0 + - - +
51A SER* 1.3 74.2 - - - +
53A GLU* 1.3 79.6 + - + +
55A ARG* 3.3 14.4 + - - +
56A LYS* 3.0 57.2 + - + +
68A VAL* 4.8 0.7 - - - +
69A ILE 3.8 2.9 - - - -
70A PRO* 3.3 38.5 - - + +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 4.9 0.2 + - - -
51A SER* 3.2 7.9 + - - +
52A TYR* 1.3 97.1 - - + +
54A HIS* 1.3 66.4 + - + +
56A LYS* 3.9 13.6 + - - +
57A LEU* 3.1 29.1 + - - +
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS* 4.5 7.3 - - + -
51A SER* 3.2 27.6 + - - +
53A GLU* 1.3 83.1 - - + +
55A ARG* 1.3 64.3 + - - +
57A LEU* 3.7 19.1 - - + +
58A ILE* 3.2 31.4 + - - +
515B TRP* 3.1 70.1 + + + -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 3.0 37.4 + - - +
10A PHE* 3.6 18.4 - - + +
11A ASP* 3.7 17.3 - - - +
35A ILE* 4.0 14.4 - - + +
36A SER 2.8 33.1 + - - +
37A THR 4.0 0.6 - - - -
38A ASP* 3.1 24.7 + - - -
41A ASN* 3.5 13.8 + - - -
48A ALA* 3.7 4.4 - - - +
50A HIS* 2.9 33.1 + - + +
51A SER 2.9 12.5 + - - +
52A TYR* 3.4 18.1 - - - +
54A HIS* 1.3 74.3 - - - +
56A LYS* 1.3 59.5 + - - +
58A ILE* 3.6 5.7 + - - +
59A LEU* 3.0 32.7 + - - +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.6 15.4 - - + +
52A TYR* 3.0 46.1 + - + +
53A GLU* 3.9 17.6 + - - +
55A ARG* 1.3 75.1 - - - +
57A LEU* 1.3 60.1 + - - +
59A LEU* 3.1 3.0 + - - +
60A GLU* 2.9 66.4 + - - +
68A VAL* 3.7 29.9 + - + -
69A ILE* 5.7 0.2 - - - +
70A PRO* 6.0 0.2 - - - -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.1 14.6 + - - +
54A HIS* 3.7 27.8 - - + +
56A LYS* 1.3 81.9 - - - +
58A ILE* 1.3 63.3 + - + +
60A GLU* 3.5 16.4 + - - +
61A THR* 3.3 20.5 + - + +
515B TRP* 4.0 18.6 - - + +
518B ILE* 3.7 33.0 - - + -
519B LYS* 5.8 8.1 - - + -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.7 30.7 - - + -
50A HIS* 5.2 9.9 - - + +
54A HIS* 3.2 20.4 + - + +
55A ARG* 4.0 5.6 - - - +
57A LEU* 1.3 78.7 - - + +
59A LEU* 1.3 66.3 + - + +
61A THR* 3.0 23.4 + - - +
62A ILE* 3.7 6.7 - - + +
513B LEU* 4.0 14.1 - - + +
514B HIS* 3.7 13.0 - - - +
515B TRP* 3.6 26.7 - - + +
518B ILE* 3.8 26.2 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.9 23.3 - - + +
13A LEU* 4.1 20.0 - - + -
21A LEU* 3.8 29.4 - - + -
33A VAL* 4.0 10.5 - - + -
35A ILE* 3.4 35.2 - - + -
55A ARG 3.0 20.7 + - - +
56A LYS 3.1 4.2 + - - +
58A ILE* 1.3 77.6 - - + +
60A GLU* 1.3 62.4 + - - +
61A THR 3.2 1.4 + - - -
62A ILE* 3.2 15.7 + - + +
65A VAL* 3.4 24.3 - - + +
68A VAL* 4.0 11.7 - - + -
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS* 2.9 54.9 + - - +
57A LEU* 3.8 14.4 - - - +
58A ILE 3.2 0.4 - - - -
59A LEU* 1.3 75.5 - - - +
61A THR* 1.3 59.1 + - + +
62A ILE 3.4 1.6 - - - -
65A VAL* 4.7 5.0 - - + +
67A GLU* 5.8 1.1 - - - -
68A VAL* 3.8 21.9 + - + +
563B ARG* 3.1 22.1 + - - -
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.3 18.6 - - + +
58A ILE 3.0 12.6 + - - +
59A LEU 3.1 1.0 - - - -
60A GLU* 1.3 78.7 - - + +
62A ILE* 1.3 61.2 + - - +
518B ILE* 3.7 28.4 - - + +
562B ILE* 3.4 31.1 - - - +
563B ARG* 2.7 40.8 + - - +
564B TYR* 4.0 18.4 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il